The invention discloses a primer sequence combination and a method for applying the primer sequence combination in PCR amplification. The amplification target in the method is specific fragments EMA inside the genome of Elizabethkingia meningoseptica, and the method shows excellent specificity and sensibility; and moreover, by using the method, the neisseria meningitidis, haemophilus influenzae, staphylococcus aureus, streptococcus pneumoniae, escherichia coli, listeria monocytogenes, mycoplasma pneumoniae, bordetella pertussis, klebsiella pneumoniae and mycobacterium tuberculosis and the other pathogenic bacteria which are likely to cause meningitis and diseases of the upper respiratory tract, and easy to be confused with the Elizabethkingia meningoseptica in an identification of bacteria, can be distinguished at one time. Additionally, the lower detection limit of the method can reach 10-4 ng per Mul.